Afghan Flag Raised Over Marja After Battling Taliban for 12 Days

After 12 days of combat, U.S. commanders said today the worst of the fighting is over and as if to prove the point they watched as the new Afghan government raised its flag over the former Taliban stronghold of Marja for the first time in years.

U.S. military commanders were upbeat, bolstered by the high turnout in the center of town to watch the flag raising ceremony and the swearing-in of Abdul Zahir Aryan as the town's new administrator.

"What you see here is Afghan government getting under way and the hard work really starts from today onwards," Major Gen. Nick Carter said.

"I think this genuinely underscores that this is a fresh start for Marja," Brig. Gen. Larry Nicholson told ABC News. U.S. officials hope Marja will be a model for new governance all over Afghanistan.

"We have said from the very beginning it's going to be a 30 day operation and I think I got to tell you it's day 12 and here we are... [I'm] pretty pleased that we are here in city center," Nicholson said.

"We are in control of all the key populated areas of Marja, we're in control of all the key infrastructure. We're still clearing a few roads out. Our focus now is on markets. Outr focus now on getting the roads open and taking care of the people," he said.

The offensive, known as Operation Moshtarak, is using a system of "clearing and holding" with the immediate introduction of government officials into areas that have been successfully cleared of Taliban.

"What we have to do now is show that the Afghan government is able to stand up and do for its people what its people expect, and that's everything from security to policing to delivering the services that Afghans expect," Carter said.

Existing police have already been removed from their positions and there are 900 Afghan Civil Order Police waiting in the wings to replace them. So far there are about 100 in place.

Mindful of the importance of civilian support Gen. Stanley McChrystal, the top commander for international forces in Afghanistan, laid out explicit guidelines for Operation Moshtarak.

"When President Karzai approved the conduct of this operation, he gave us some specific guidance and that guidance was to continue to protect the people of Afghanistan. So this operation has been done with that in mind," McChrystal told reporters at the outset of the offensive.

Taliban Left Behind at Least 100 Booby Traps

Adhering to these strict rules of engagement and faced with at least a hundred hidden bombs and booby traps has meant that the process of clearing the town of insurgents has been slow.

The Taliban's most important weapon has been the IED (Improvised Explosive Device)and it's been responsible for most of the coalition casualties. Some civilians have also been killed by IED's.

There are conflicting accounts as to how many civilians have been killed so far. The Afghan human rights commission say as many as 28 people have died, but the U.S. puts the figure lower at 20. The biggest casualty count came when a stray NATO rocket hit a house killing 12, including women and children.

Thirteen coalition and three Afghan soldiers have been killed in the offensive so far and despite the fanfare in Marja's main market today some fighting continues. A senior U.S. military official indicated to ABC News that the fighting would continue for several more weeks.

The mass assault in southern Helmand province, with 15,000 NATO and Afghan troops, is the largest military operation in Afghanistan since the U.S.-led ouster of the Taliban regime in 2001.

Miguel Marquez, Luis Martinez and the Associated Press contributed to this report.